VizCNV

This is a shiny app for chromosomal copy number variant analysis. It can parse the vcf file with SV calls, visualize CNV and B-allele frequency and genetic phasing information interactively.

Prerequisites

R version >= 3.6.3 Following R libraries are required:

Shifting level models based segmentation is performed using SLMSuite.

Launch app on local with the main branch:

shiny::runGitHub(repo = "BCM-Lupskilab/VizCNV")

or Launch app on local with the dev branch:

shiny::runGitHub(repo = "cluhaowie/VizCNV",ref="dev")

A docker image is public available through docker hub docker pull duclare123/vizcnv_dev

Upload the required file from local file systerm: gif1

If launch the app on cloud or on server, input file need to be upload due to access restriction.

Visualize the CNV calls in table format, read depth plot and B-allele frequency together: gif1

The app require read depth file as the input: A output from mosedepth can be used example of generate the read depth file for 1Kb window size would be:

mosdepth -n --fast-mode --by 1000 sample.wgs $sample.wgs.cram